So basically you have a VPN from the remote site to the host site, assuming simple networking issues like VLAN are not an issue or at least taken into consideration with routing, this is actually quite common and normal... We see it over VPNs, MPLS circuits, T-1's, and other dedicated connections. Just remember to have sufficient bandwidth and quality of connection and your good to go. A PC/client based VPN will NOT work though, this needs to be a hardware based solution, router to router being the most common.
The whole problem with remote phone on the 3300 is NAT since the 3300 does not support it directly. A VPN doesn't use NAT for the traffic between nodes across the VPN tunnel, so the phones will work fine.